update pre-commit, use numpy>=2 and hoomd>=5

Author: chrisjonesBSU

environment-dev.yml

@@ -4,11 +4,11 @@ channels:
 dependencies:
 - freud >=3.0,<3.2
 - gsd >=3.0
-- hoomd >=4.0,<5.0
+- hoomd >=5.0
 - python >=3.10
 - pandas
 - cmeutils >=1.3
-- numpy <2.0
+- numpy >=2.0,<2.3
 - more-itertools
 - pytest
 - pytest-cov

environment.yml

@@ -4,9 +4,9 @@ channels:
 dependencies:
 - freud >=3.0,<3.2
 - gsd >=3.0
-- hoomd >=4.0,<5.0
+- hoomd >=5.0
 - python >=3.10
 - pandas
 - cmeutils >=1.3
-- numpy <2.0
+- numpy >=2.0,<2.3
 - more-itertools

msibi/utils/smoothing.py

@@ -37,7 +37,7 @@ def savitzky_golay(
 
     order_range = range(order + 1)
     half_window = (window_size - 1) // 2
-    b = np.mat(
+    b = np.asmatrix(
         [[k**i for i in order_range] for k in range(-half_window, half_window + 1)]
     )
     m = np.linalg.pinv(b).A[deriv] * 1**deriv * factorial(deriv)

setup.cfg

@@ -23,5 +23,3 @@ omit =
 [bumpversion:file:msibi/__version__.py]
 
 [bumpversion:file:pyproject.toml]
-
-#[bumpversion:file:docs/conf.py]